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   <title>Completeness of distance restraints; complchk</title>
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<h1>
Aqua program module</h1>

<h2>
Completeness of distance restraints</h2>

<h3>
complchk script</h3>

<hr>
<p>The completeness check and its application to a large set of structures
is described in:
<ul>
<li>
J.F. Doreleijers, M.L. Raves, J.A.C. Rullmann &amp; R. Kaptein. "Completeness
of NOEs in proteins: a statistical analysis of NMR data"
<i>J. Biomol.
NMR</i> (1999) <b>14</b>, 123-132.</li>
</ul>

<hr>
<h3>
Overview</h3>
The 'complchk' script checks the completeness of NOE distance restraints
using a method described elsewhere (see 'qhelp <a href="AquaCompl.html">qcompl</a>').
<p>The script first runs '<a href="../doc/aqpc.txt">aqpc</a>', followed
by the AquaCompl module itself.
<p>The command syntax is very much like that of 'aqpc':
<p>&nbsp;&nbsp;&nbsp; complchk&nbsp; [options]&nbsp; COORDINATE_FILE&nbsp;
[RANGES_FILE]
<br>&nbsp;
<p>The options (can be given in any order) are:
<p>&nbsp;&nbsp;&nbsp; [-c]&nbsp; [-r&nbsp; RESTRAINT_PREFIX]&nbsp; [-ext]&nbsp;
[-xplor|molmol]&nbsp; [-r6ave|r6sum value] [-terseness value]
<br>&nbsp;
<p><b>COORDINATE_FILE</b> is the name of the coordinates file in either
PDB or BIOSYM format (car or multi-line arc). The name of the COORDINATE_FILE
provides a project name for 'aqpc' and 'complchk'. This project name is
derived from COORDINATE_FILE by removing extension and path. The root name
of all output files is the project name.
<p><b>[ranges-file]</b> is the name of an (optional) file specifying which
models and residue ranges are to be included in the calculations (see 'qhelp
<a href="../doc/ranges.txt">ranges</a>').
<p><b>[-r] </b>is used to specify the prefix of the converted restraint
file(s), i.e. the root name of the files produced by 'qconvert'. This option
can be omitted if the prefix and project name are identical.
<p><b>[-c]</b> prevents cleanup of the working files. This will speed up
the calculation if you repeat the analysis for COORDINATE_FILE, e.g. with
a different restraint file or a (different) RANGES_FILE. (Note that in
this case the output files will be overwritten since they have the same
project name!). If, however, the contents of COORDINATE_FILE have changed,
all intermediate files should be removed before rerunning the program;
this is accomplished by the 'qclean' command, see 'qhelp <a href="../doc/qclean.txt">qclean</a>'.
<p><b>[-ext]</b> forces the program to use the external (original) names
to match restraint atoms to coordinate atoms (default is to use internal
names; see 'qhelp <a href="../doc/names.txt">names</a>')
<p><b>[-xplor]</b> forces the program to use the correct library for XPLOR-style
PDB coordinate files, see 'qhelp <a href="../doc/xplor.txt">xplor</a>'.
<p><b>[-terseness value]</b> is used to specify decreasing verbosity for
normal output to most log files. The level can be set to 0 through 9 with
9 specifying the least verbose output. This parameter does NOT affect warning
and error messages which will always be presented. The standard value of
terseness is 0 (most verbose). The following scheme describes the output
that can be expected for each range of values:
<ul>&nbsp;
<table>
<tr>
<td VALIGN=TOP>0-2</td>

<td VALIGN=TOP>verbose&nbsp;</td>

<td VALIGN=TOP>All output except debugging information will be presented.</td>
</tr>

<tr>
<td VALIGN=TOP>3-5</td>

<td VALIGN=TOP>curbed&nbsp;</td>

<td VALIGN=TOP>The output is somewhat limited. Program timing information,
status reports on the opening and closing of files, the values to options
set and more details are not echoed. A level below 6 will also prevent
some long listings but still have the program echo a summary line that
would not exist with a higher value.</td>
</tr>

<tr>
<td VALIGN=TOP>6-9&nbsp;</td>

<td VALIGN=TOP>terse&nbsp;</td>

<td VALIGN=TOP>Least amount of output will be presented. Even a terseness
value of 9 will not prevent warnings and errors from being reported. Information
on e.g. environmental values, values to menu options etc. will not be echoed
at this level. A value of 9 will even prevent the menu from being shown
so might not be very useful for interactive work outside the aqpc script.</td>
</tr>
</table>
</ul>
<b>[-molmol] </b>forces the program to use the correct library for MOLMOL-style
PDB coordinate files.
<p><b>[-r6ave]</b> use R<sup>-6</sup> averaging for all NOE restraints.
<p><b>[-r6sum value] </b>use R<sup>-6</sup> summing for all NOE restraints;
value specifies the number of monomers. The -r6ave or -r6sum options only
influence the redundancy check.
<p>
<hr WIDTH="100%">
<p><b>Processing options</b>:
<p>Options, like the threshold for the maximum distance,&nbsp; may be changed
by setting an option in the text file 'compl.cmm' in your working directory.
If the file does not exist, you can create it. The format of the option
is as follows:
<p>&nbsp;&nbsp;&nbsp; set max_dist_prs VALUE
<p>The computation time increases approximately quadratically with this
value.
<br>&nbsp;
<p><i>Other processing options:</i>
<br>&nbsp;
<table BORDER CELLPADDING=10 NOSAVE >
<tr NOSAVE>
<td NOSAVE>
<center><b>Option</b></center>
</td>

<td>
<center><b>Type</b></center>
</td>

<td>
<center><b>Default&nbsp;</b></center>
</td>

<td>
<center><b>Description</b></center>
</td>
</tr>

<tr NOSAVE>
<td>min_dist_prs</td>

<td>real</td>

<td NOSAVE>2.0</td>

<td>Minimum distance for pairs. Pairs with distances below this will be
categorized in the lowest shell as well.</td>
</tr>

<tr>
<td>max_dist_prs</td>

<td>real</td>

<td>4.0</td>

<td>As mentioned above. Maximum distance for pairs. If the average distance
between observable atoms is below this threshold an observable pair will
be added.</td>
</tr>

<tr>
<td>numb_shells_prs</td>

<td>integer</td>

<td>4</td>

<td>Number of shells to categorize the pairs.</td>
</tr>

<tr>
<td>min_dist_rst</td>

<td>real</td>

<td>2.0</td>

<td>Minimum distance for restraints. Restraints with distances below this
will be categorized in the lowest shell as well.</td>
</tr>

<tr>
<td>max_dist_rst</td>

<td>real</td>

<td>4.0</td>

<td>Maximum distance for restraints. Restraints with distances above this
will be categorized in the highest shell as well.</td>
</tr>

<tr>
<td>numb_shells_rst</td>

<td>integer</td>

<td>4</td>

<td>Number of shells to categorize the restraints.</td>
</tr>

<tr>
<td>use_intra</td>

<td>logical</td>

<td>true&nbsp;</td>

<td>Intra-residual restraints are used.</td>
</tr>

<tr>
<td>detail</td>

<td>logical</td>

<td>true</td>

<td>More detailed output is given. A listing per observable atom is printed
in the ".comp" file. The data blocks COMPLETENESS_PER_RESATOM and COMPLETENESS_PER_ATOM
are generated in this file.</td>
</tr>

<tr>
<td>terseness</td>

<td>integer</td>

<td>0</td>

<td>The higher this value the more terse the output will become. See description
above.</td>
</tr>

<tr>
<td>double_count</td>

<td>logical</td>

<td>false</td>

<td>The restraints and pairs are scored for each atom, possibly scored
double in case the atoms are of the same class. This applies to all data
blocks except SUMMARY_OVERALL, COMPLETENESS_PER_SHELL, COMPLETENESS_PER_CLASS,
and COMPLETENESS_PER_RESIDUE (in case use_intra is true).</td>
</tr>

<tr>
<td>anal_ssa</td>

<td>logical</td>

<td>true</td>

<td>The stereospecific assignments that are possible and found according
to the restraints are compared to each other. The results are then given
in blocks: SSA_PER_TYPE, SSA_PER_ATOM_TYPE, SSA_PER_ATOM.</td>
</tr>

<tr NOSAVE>
<td>atominp</td>

<td>string</td>

<td NOSAVE>ob_standard</td>

<td>An Aqua set containing the definition of observable atoms. Several
definitions are included in the <a href="../data">data directory.</a></td>
</tr>
</table>

<br>&nbsp;
<p><i>Processing option for <a href="../doc/AquaRedun.txt">redundancy check</a>
(intra-residual contacts only):</i>
<br>&nbsp;
<br>&nbsp;
<table BORDER CELLPADDING=10 NOSAVE >
<tr>
<td>
<center><b>Options</b></center>
</td>

<td>
<center><b>Type</b></center>
</td>

<td>
<center><b>Default</b></center>
</td>

<td>
<center><b>Description</b></center>
</td>
</tr>

<tr NOSAVE>
<td>thresh</td>

<td>real</td>

<td>9999.9</td>

<td NOSAVE>Threshold value for redundancy check; if 9999.9 only fixed distances
will be removed (which is appropriate here, see <a href="compl_method.html">methods</a>).</td>
</tr>

<tr>
<td>savpseu</td>

<td>logical</td>

<td>false</td>

<td>Restraints including pseudoatoms are skipped if this option is set
to true. This option is automatically set to true if option -r6ave or -r6sum
is specified.</td>
</tr>
</table>

<br>&nbsp;
<p>
<hr>
<p><b>NOTES</b>
<ul>
<li>
The completeness and the redundancy check can also be performed by the
AQUA <a href="../server/.">server</a>.</li>

<li>
More documentation is available on the <a href="compl_method.html">methods</a>
and <a href="compl_output.html">output</a> of the program module AquaCompl.</li>

<li>
More documentation is available on the <a href="../doc/redun_method.txt">methods</a>
and <a href="../doc/redun_output.txt">output</a> of the redundancy check
program module <a href="../doc/AquaRedun.txt">AquaRedun</a> and the script
<a href="../doc/redunchk.txt">redunchk</a>.</li>
</ul>

<hr>
<p>Contact the <a href="mailto:jurgenfd@gmail.com">author</a> for help,
when required.
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